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Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with Vaniprevir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100mM MES buffer pH 6.5, 4% (w/v) ammonium sulfate, 20-26% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.119 α = 90 b = 58.403 β = 90 c = 60.016 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 2014-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 33.3 94.1 0.062 19.5 4.5 7436
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 97 0.139 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3m5m 2.4 33 6559 744 91.18 0.1871 0.1819 0.1954 0.2329 0.2396 RANDOM 21.417
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.35 -0.03 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_4_deg 12.596 r_dihedral_angle_1_deg 6.557 r_angle_refined_deg 1.606 r_mcangle_it 1.455 r_angle_other_deg 1.277 r_mcbond_it 0.817 r_mcbond_other 0.809 r_chiral_restr 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_4_deg 12.596 r_dihedral_angle_1_deg 6.557 r_angle_refined_deg 1.606 r_mcangle_it 1.455 r_angle_other_deg 1.277 r_mcbond_it 0.817 r_mcbond_other 0.809 r_chiral_restr 0.289 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 64
Software Software Software Name Purpose xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction